"Duress of circumstances" is available as a defence for anybody accused of a crime. I would presume that would cover many cases of undercovers committing minor crimes to maintain their covers in threatening circumstances.

I'm not aware that it's ever been a real issue, eg. I'm not sure if there's any suggestion of Bob Lambert being prosecuted for his alleged involvement in firebombing Debenhams.

Edit: I'm a bit confused about what the actual legal implications of this "guidance" are. IIUC it's about guidance given to MI5 agents, as such I suppose in theory the legal implication is that if they commit "authorised" crimes they could argue in court that it's their employer's responsibility.